Data from: Pesticide and pathogen exposure causes idiosyncratic gene expression responses across four diverse North American bumble bee species

Bumble bee populations of certain species have been declining precipitously in North America over several decades. Hypotheses for declines include exposure to the fungal pathogen Nosema bombi and neonicotinoid pesticides. Importantly, populations of some bumble bee species remain stable despite their presumed exposure to these same stressors. Here we hypothesize that declining and stable species, respectively, exhibit distinct responses to N. bombi and neonicotinoid pesticides, detectable as differential gene expression profiles. To test this, we exposed developing larvae from colonies of Bombus occidentalis (declining) and B. impatiens (stable) to N. bombi and to the neonicotinoid imidacloprid, plus a combination of both. RNA-seq analysis revealed almost no overlap between these species in gene expression responses to the individual stressors. Combined-stressor effects were more similar, but nevertheless differed significantly in differentially expressed genes and in gene coexpression network modules. To test whether the molecular responses correlated within declining and stable species, we carried out quantitative PCR on twenty target genes and included a second pair of species, B. terricola (declining) and B. griseocollis (stable). Results showed no correlation with decline or stable status, with each of the four species exhibiting species-specific responses. Overall, these results highlight that generalizing causes of decline across different species may be misleading, as diverse species respond in a species-specific manner to particular environmental stressors.